Yes replying to you only was in error. I will take a look at the Python
project you mentioned. I also got the Jekyll code going by regressing
to a previous version.
Thanks again for the feedback.
On 1/15/24 10:19, Peter Cock wrote:
Whoops - I missed that as I initially assumed hilberglm was
someone else. Sorry. By the way, I'm happy to take this thread
back to the mailing list if replying to just me was in error.
In Biopython we use a tool called blacken-docs to apply the same
automated formatting style (defined in a tool called black) to the
examples in our documentation that we use in the main code:
https://pypi.org/project/blacken-docs/
I don't know if there is something similar possible in Java?
As to the automated builds with Jekyll, there are likely some
fixes made on https://github.com/biopython/biopython.github.io/
which can be copied over.
Peter
On Mon, Jan 15, 2024 at 4:06 PM Gary Murphy <hilbert...@gmail.com> wrote:
Thank you for getting back to me so quickly. Yes, I am the Gary Murphy
that forked the source to take a look at it and understand how to build
it. I should have posted the official github URL instead of my fork.
I have some code that reads FASTA files using Java streams that I
haven't submitted a pull request for, but I wanted to have a handle on
how to document it if it was accepted. Specifically,
_wiki/BioJava_CookBook_Core_FastaReadWrite.md is the one I updated
locally, but haven't pushed. I also noted a lot of formatting errors on
the source code in the Cookbook, so I would be changing those only when
I update a page... a global update would be pretty time-consuming.
More generally, since I am learning the code base, I thought it would be
beneficial for me to add documentation when I learn how to do things in
the normal course of my job that I had to jump into the source code
and/or test cases to understand.
The first thing I would be updating is how to update the documentation.
The Jekyll docker container is broken out of the gate, so I had to
figure out how to get the build server running locally to ensure my
changes were getting rendered properly.
I have spent some time in the tutorials. They are extremely helpful and
seem to be more recently updated.
On 1/15/24 09:49, Peter Cock wrote:
I'd guess the source you want is https://github.com/biojava/biojava.github.io
but Gary Murphy's version https://github.com/hilbertglm/biojava.github.io.git
looks to be the same right now - this is the main BioJava website and
it does indeed look not to have been updated recently. This includes what
used to be the wiki content (including the cookbook), now as markdown pages.
This repository also includes API documentation.
What specifically did you want to change here? e.g. An example URL
See also https://github.com/biojava/biojava-tutorial which has been changed
much more recently.
Peter
On Mon, Jan 15, 2024 at 2:53 PM Gary Murphy <hilbert...@gmail.com> wrote:
Sorry if this is a duplicate, but the mailing list confirmation got moved to
the spam folder, so I don't know if this original e-mail was honored.
-----
I am new to the biojava community, so I thought I would be a good candidate to
update some of the documentation as I discover how to accomplish my goals with
biojava.
I got the source for the Cookbook
(https://github.com/hilbertglm/biojava.github.io.git), and it seems like it is
a bit out of date with quite a few formatting issues for the source code.
Before I start...
Is there any effort I should be aware of for a new one, or is anyone actively
working on it? If so, we should coordinate efforts
Does anyone have any issue with my removing the non-breaking spaces in the
source code. It shows as [NBSP] in Intellij, so it is going to be tough to do
any editing on that.
Any thoughts would be appreciated.
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